Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives

The structural, dynamical, and recognition properties of antiparallel DNA triplexes formed by the antiparallel d(G#G.C), d(A#A.T), and d(T#A.T) motifs (the pound sign and dot mean reverse-Hoogsteen and Watson-Crick hydrogen bonds, respectively) are studied by means of "state of the art" molecular dynamics simulations. Once the characteristics of the helix are defined, molecular dynamics and thermodynamic integration calculations are used to determine the expected stabilization of the antiparallel triplex caused by the introduction of 8-aminopurines. Finally, oligonucleotides containing 8-aminopurine derivatives are synthesized and tested experimentally using several approaches in a variety of systems. A very large stabilization of the triplex is found experimentally, as predicted by simulations. These results open the possibility for the use of oligonucleotides carrying 8-aminopurines to bind single-stranded nucleic acids by formation of antiparallel triplexes.     

Effect of the rhenium additive to VOx/TiO2 and MoOx/TiO2 catalysts on their properties in oxidative dehydrogenation of propane

VO_x/TiO₂ and MoO_x/TiO₂ catalysts with the addition of Re (Re/V or Mo = 0.5) were synthetized and tested in oxidative dehydrogenation of propane and in reduction by propane. XPS measurements showed depletion of the surface in Re. The Re additive does not affect the total conversion of propane, but increases the selectivity to propene. The effect is more pronounced for the MoO_x/TiO₂ catalyst. The increase in the selectivity to propene is accompanied with the increase in the reducibility of the catalysts.     

A synthetic divalent cholera toxin glycocalix[4]arene ligand having higher affinity than natural GM1 oligosaccharide

A high-affinity ligand of cholera toxin, the divalent glycocalix[4]arene 1, was obtained by exploiting a combination of structure-based design of glycomimetic monovalent ligands and affinity enhancements by multivalent presentation through a calix[4]arene scaffold. It exhibits a slightly higher affinity for the toxin than its natural ligand, the GM1 oligosaccharide.     

Determination of complex formation constants by phase sensitive alternating current polarography: Cadmium-polymethacrylic acid and cadmium-polygalacturonic acid

The use of phase sensitive alternating current polarography (ACP) for the evaluation of complex formation constants of systems where electrodic adsorption is present has been proposed. The applicability of the technique implies the previous selection of the phase angle where contribution of capacitive current is minimized. This is made using Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) in the analysis of ACP measurements at different phase angles. The method is checked by the study of the complexation of Cd by polymethacrylic (PMA) and polygalacturonic (PGA) acids, and the optimal phase angles have been ca. −10° for Cd-PMA and ca. −15° for Cd-PGA systems. The goodness of phase sensitive ACP has been demonstrated comparing the determined complex formation constants with those obtained by reverse pulse polarography, a technique that minimizes the electrode adsorption effects on the measured currents.     

A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.     

Analysis of gadobenate dimeglumine by capillary zone electrophoresis coupled with electrospray-mass spectrometry

Highly reliable and accurate analytical methods are needed for the determination of magnetic resonance imaging (MRI) contrast agents in complex matrices of clinical interest. We demonstrate the reliability of capillary zone electrophoresis (CZE) coupled with electrospray ionization-mass spectrometry (ESI-MS) for the analysis of MultiHance (gadobenate dimeglumine), a gadolinium-based MRI agent. A sheath liquid interface connected the CE system with an electrospray mass spectrometer equipped with an ion-trap analyzer. CZE with ultraviolet (CZE-UV) and with mass detection (CZE-MS) were compared by analyzing gadobenate dimeglumine and the free ligand diluted in water and in biological fluids (i.e., human serum and urine). The optimization of some relevant CZE-MS parameters was accomplished, like CE buffer composition, sheath liquid composition and flow, and type and length of the separation capillary. CZE-UV was highly influenced by the biological sample components, which hindered a reliable quantification of both gadobenate and free ligand in serum and urine. In CZE-MS, on the other hand, the electrophoretic runs turned out to be independent of the clinical matrices, due to the informative potential and to the selectivity of MS detection.     

Total spontaneous resolution of chiral covalent networks from stereochemically labile metal complexes

Stereochemically labile copper and zinc complexes with the N,N'-dimethylethylenediamine ligand (dmeda) have been shown to be promising precursors for the total spontaneous resolution of chiral covalent networks. (N,N')-[Cu(NO3)2(dmeda)]infinity crystallises as a conglomerate and yields either enantiopure (R,R)-1 or enantiopure (S,S)-1. A mixed-valence copper(I/II) complex, [{Cu(II)Br2(dmeda)}3(Cu(I)Br)2]infinity (2), which crystallises as a pair of interpenetrating chiral (10,3)-a nets, is formed from CuBr, CuBr2 and dmeda. One net contains ligands with solely (R,R) configuration and exhibits helices with (P) configuration while the other has solely (S,S)-dmeda ligands and gives rise to a net in which the helices have (M) configuration. The whole crystalline arrangement is racemic, because the interpenetrating chiral nets are of opposite handedness. With zinc chloride (R,S)-[ZnCl(dmeda)2]2[ZnCl4] (3) is obtained, which is a network structure, although not chiral. Total spontaneous resolution of stereochemically labile metal complexes formed from achiral or racemic building blocks is suggested as a viable route for the preparation of covalent chiral networks. Once the absolute structure of the compound has been determined by X-ray crystallography, a quantitative determination of the enantiomeric excess of the bulk product can be undertaken by means of solid-state CD spectroscopy.     

Nonspecific interactions of a carboxylate-substituted PPE with proteins. A cautionary tale for biosensor applications

Two carboxylate-substituted, fluorescent (Phi = 0.08), water-soluble poly(p-phenyleneethynylene)s (PPE) and a water-soluble model compound were exposed to a series of proteins and bovine serum. While the anionic PPEs do not have any specific binding sites, they form stable complexes with histone, lysozyme, myoglobin, and hemoglobin. The complex formation was evidenced by fluorescence quenching. Bovine serum albumin does not quench the fluorescence of the PPEs but enhances it, probably due to its surfactant character. These results imply that the use of charged conjugated polymers as biosensors, while an attractive proposition, has to take into account strong nonspecific interactions between conjugated polymers and the host of proteins that is found in cells and complex biological fluids.     

Enzymatic hydrolysis of heterocyclic nitriles

Chemoselective hydrolysis of heterocyclic nitriles can be achieved by an easy to use immobilized biocatalyst prepared from Rhodococcus sp. Pyrimidine-2-carbonitrile ( 2a ) and 3-chloropyridazine-4-carbonitrile ( 4a ) were converted into the corresponding amides while from 2-ethoxycarbonyl-4-pyridinecarbonitrile ( 1a ), 6-methylpyridazine-3-carbonitrile ( 3a ), 3-chloropyridazine-4-carbonitrile ( 4a ), 3-ethoxycarbonyl-4,5-dihydroisoxazole-5-carbonitrile ( 8a ), indole-3-carbonitrile ( 9a ) and indole-3-ylacetonitrile ( 10a ) the acids were formed.     

Electron-transfer in molecular functional materials

We discuss electron-transfer processes that govern the physics of several materials or systems of interest for advanced applications. The discussion touches upon several topics, ranging from solvatochromism to solvent-induced symmetry breaking, from excitonic to cooperative effects in molecular crystals, from phase transitions to vibrational contributions to the dielectric constant in organic materials, from spectroscopy to molecular transport. In all these diverse systems electron transfer (ET) plays a major role and is discussed with reference to simple models for delocalized charges.